VIGGS:Variant information

Chr10:3036524 - 3041519

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
3036871	G	A	63	2814.77	1.00	UPSTREAM(\|3974\|\|None\|Vigan.10G031300.01), UTR_5_PRIME(\|33\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3036880	A	G	63	2784.77	1.00	UPSTREAM(\|3983\|\|None\|Vigan.10G031300.01), UTR_5_PRIME(\|24\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3036933	G	C	56	2123.77	1.00	SYNONYMOUS_CODING(SILENT\|gtG/gtC\|V10\|None\|Vigan.10G031400.01), UPSTREAM(\|4036\|\|None\|Vigan.10G031300.01)	Vigna nepalensis
3036975	T	C	51	1800.77	1.00	SYNONYMOUS_CODING(SILENT\|gcT/gcC\|A24\|None\|Vigan.10G031400.01), UPSTREAM(\|4078\|\|None\|Vigan.10G031300.01)	Vigna nepalensis
3037320	C	T	49	1846.77	1.00	SYNONYMOUS_CODING(SILENT\|ctC/ctT\|L139\|None\|Vigan.10G031400.01), UPSTREAM(\|4423\|\|None\|Vigan.10G031300.01)	Vigna nepalensis
3037410	T	C	54	2134.77	1.00	SYNONYMOUS_CODING(SILENT\|gcT/gcC\|A169\|None\|Vigan.10G031400.01), UPSTREAM(\|4513\|\|None\|Vigan.10G031300.01)	Vigna nepalensis
3037809	A	G	33	1214.77	1.00	SYNONYMOUS_CODING(SILENT\|ccA/ccG\|P302\|None\|Vigan.10G031400.01), UPSTREAM(\|4912\|\|None\|Vigan.10G031300.01)	Vigna nepalensis
3037932	G	A	44	1729.77	1.00	SYNONYMOUS_CODING(SILENT\|gcG/gcA\|A343\|None\|Vigan.10G031400.01)	Vigna nepalensis
3038292	G	A	44	1990.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3039104	G	A	58	2364.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3039353	T	C	51	2060.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3039750	C	T	59	2381.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040532	G	T	59	2626.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040535	T	C	59	2626.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040600	A	T	62	2460.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040626	T	A	60	2725.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040651	C	T	57	2546.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040682	T	C	60	2316.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040784	T	C	47	2131.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040839	C	T	59	2529.77	1.00	SYNONYMOUS_CODING(SILENT\|aaC/aaT\|N606\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040863	G	A	57	2577.77	1.00	SPLICE_SITE_REGION(\|\|\|None\|Vigan.10G031400.01), SYNONYMOUS_CODING(SILENT\|acG/acA\|T614\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040886	T	A	45	2131.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040908	C	T	49	2266.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040922	T	A	49	2403.77	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3041032	T	C	53	2175.77	1.00	UTR_3_PRIME(\|5\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3041210	T	C	57	2276.77	1.00	UTR_3_PRIME(\|183\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3041357	A	G	55	2054.77	1.00	UTR_3_PRIME(\|330\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3041491	C	T	59	2316.77	1.00	UTR_3_PRIME(\|464\|\|None\|Vigan.10G031400.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
3038967	C	CGGAA	52	2341.73	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3039779	A	AT	64	2540.73	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3039815	A	AG	62	2165.73	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040763	C	CT	39	1815.73	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3040891	TCATCA	T	47	2167.73	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3041057	AG	A	55	1886.73	1.00	UTR_3_PRIME(\|31\|\|None\|Vigan.10G031400.01)	Vigna nepalensis
3041068	AAC	A	56	1237.74	0.91	UTR_3_PRIME(\|42\|\|None\|Vigan.10G031400.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
3038300	(AT)28	(AT)13	45	1988.73	1.00	INTRON(\|\|\|None\|Vigan.10G031400.01)	Vigna nepalensis